# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Nov 14 07:57:03 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (2S)-2-chloro-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](Cl)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 03H  03H  "(2S)-2-chloro-4-methylpentanoic acid"  ligand  19  9  .  2022-11-14  2022-11-14
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_03H
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 03H  CL   CL  CL     0  -0.200   0.5222   1.8111   0.1779
 03H  C1   C   C      0   0.441   1.8306  -0.6197  -0.1652
 03H  O1   O   OC    -1  -0.610   1.8909  -1.8446   0.0590
 03H  C2   C   CH1    0  -0.396   0.4975   0.0051   0.3129
 03H  O2   O   O      0  -0.579   2.6774   0.0986  -0.7100
 03H  C3   C   CH2    0  -0.393  -0.6908  -0.5523  -0.4553
 03H  C4   C   CH1    0  -0.228  -2.0733  -0.0459  -0.0424
 03H  C5   C   CH3    0  -0.651  -3.1394  -0.7518  -0.8755
 03H  C6   C   CH3    0  -0.662  -2.3379  -0.2370   1.4470
 03H  H2   H   HCH1   0   0.276   0.3820  -0.1962   1.3790
 03H  H3   H   HCH2   0   0.231  -0.5442  -0.3689  -1.5245
 03H  H3A  H   HCH2   0   0.229  -0.6603  -1.6378  -0.3202
 03H  H4   H   HCH1   0   0.215  -2.1290   1.0249  -0.2629
 03H  H5   H   HCH3   0   0.212  -3.1253  -1.8302  -0.6979
 03H  H5A  H   HCH3   0   0.225  -4.1386  -0.3884  -0.6301
 03H  H5B  H   HCH3   0   0.224  -2.9826  -0.5916  -1.9440
 03H  H6   H   HCH3   0   0.213  -2.2215  -1.2845   1.7374
 03H  H6A  H   HCH3   0   0.226  -1.6620   0.3571   2.0637
 03H  H6B  H   HCH3   0   0.228  -3.3549   0.0653   1.7016

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 03H  CL  C2   single  1.811  0.020  1.785
 03H  O2  C1   deloc   1.237  0.020  1.259
 03H  O1  C1   deloc   1.247  0.020  1.259
 03H  C1  C2   single  1.548  0.020  1.527
 03H  C2  C3   single  1.521  0.020  1.527
 03H  C2  H2   single  0.970  0.020  1.090
 03H  C3  C4   single  1.529  0.020  1.527
 03H  C3  H3   single  0.970  0.020  1.090
 03H  C3  H3A  single  0.970  0.020  1.090
 03H  C4  C6   single  1.525  0.020  1.527
 03H  C4  C5   single  1.526  0.020  1.527
 03H  C4  H4   single  0.970  0.020  1.090
 03H  C5  H5   single  0.970  0.020  1.090
 03H  C5  H5A  single  0.970  0.020  1.090
 03H  C5  H5B  single  0.970  0.020  1.090
 03H  C6  H6   single  0.970  0.020  1.090
 03H  C6  H6A  single  0.970  0.020  1.090
 03H  C6  H6B  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 03H  O2   C1  C2   119.42  3.000
 03H  C2   C1  O1   112.50  3.000
 03H  O2   C1  O1   128.08  3.000
 03H  H2   C2  C3   110.08  3.000
 03H  H2   C2  C1   108.57  3.000
 03H  C3   C2  C1   111.65  3.000
 03H  H2   C2  CL   104.97  3.000
 03H  C3   C2  CL   109.78  3.000
 03H  C1   C2  CL   111.57  3.000
 03H  H3A  C3  H3   106.44  3.000
 03H  H3A  C3  C4   108.68  3.000
 03H  H3   C3  C4   109.24  3.000
 03H  H3A  C3  C2   106.22  3.000
 03H  H3   C3  C2   109.11  3.000
 03H  C4   C3  C2   116.66  3.000
 03H  H4   C4  C6   108.09  3.000
 03H  H4   C4  C5   107.88  3.000
 03H  C6   C4  C5   110.74  3.000
 03H  H4   C4  C3   108.39  3.000
 03H  C5   C4  C3   109.33  3.000
 03H  C6   C4  C3   112.28  3.000
 03H  H5B  C5  H5A  107.62  3.000
 03H  H5B  C5  H5   107.58  3.000
 03H  H5A  C5  H5   107.68  3.000
 03H  H5B  C5  C4   111.48  3.000
 03H  H5A  C5  C4   111.28  3.000
 03H  H5   C5  C4   111.02  3.000
 03H  H6B  C6  H6A  107.14  3.000
 03H  H6B  C6  H6   107.62  3.000
 03H  H6A  C6  H6   107.80  3.000
 03H  H6B  C6  C4   110.79  3.000
 03H  H6A  C6  C4   112.12  3.000
 03H  H6   C6  C4   111.17  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 03H  Var_01  C6   C4  C3  C2   -54.34  30.0  3
 03H  Var_02  C5   C4  C3  C2  -177.66  30.0  3
 03H  Var_03  H4   C4  C3  C2    64.99  30.0  3
 03H  Var_04  H6   C6  C4  C3   -56.31  30.0  3
 03H  Var_05  H6A  C6  C4  C3    64.43  30.0  3
 03H  Var_06  H6B  C6  C4  C3  -175.92  30.0  3
 03H  Var_07  H5   C5  C4  C3    62.03  30.0  3
 03H  Var_08  H5A  C5  C4  C3  -178.05  30.0  3
 03H  Var_09  H5B  C5  C4  C3   -57.89  30.0  3
 03H  Var_10  H3   C3  C4  C5    58.07  30.0  2
 03H  Var_11  H3A  C3  C4  C5   -57.68  30.0  2
 03H  Var_12  H6   C6  C4  C5    66.22  30.0  3
 03H  Var_13  H6A  C6  C4  C5  -173.04  30.0  3
 03H  Var_14  H6B  C6  C4  C5   -53.40  30.0  3
 03H  Var_15  H3   C3  C4  C6  -178.61  30.0  2
 03H  Var_16  H3A  C3  C4  C6    65.64  30.0  2
 03H  Var_17  H5   C5  C4  C6   -62.20  30.0  3
 03H  Var_18  H5A  C5  C4  C6    57.72  30.0  3
 03H  Var_19  H5B  C5  C4  C6   177.88  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 03H  chir_01  C2  CL  C1  C3  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 03H  plan-1  C1  0.020
 03H  plan-1  O1  0.020
 03H  plan-1  C2  0.020
 03H  plan-1  O2  0.020

